Protein Data Bank: Difference between revisions
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==Remediation== | ==Remediation== | ||
Periodically, the PDB remediates its archived data files. Remediation improves consistency and nomenclature and removes some errors. Remediation involves changes in the PDB data format. Remediations occurred in August, 2007 and March, 2009. Details will be found at the [http://www.wwpdb.org/docs.html World Wide PDB]. | Periodically, the PDB remediates its archived data files. Remediation improves consistency and nomenclature and removes some errors. Remediation involves changes in the [[Atomic_coordinate_file#PDB_Data_Format|PDB data format]]. Remediations occurred in August, 2007 and March, 2009. Details will be found at the [http://www.wwpdb.org/docs.html World Wide PDB]. | ||
Here are some examples of changes that occurred in remediations affecting the PDB format. Prior to August, 2007, both DNA and RNA nucleotides were named A, C, G, T, and U. After August, 2007, DNA nucleotides were changed to DA, DC, DG, DT and DU, while RNA nucleotides continued to use the older one-letter names. (An example of a model that contains both DNA and RNA is [[104d]].) This change required changes in software packages such as [[Jmol]], and left unmaintained packages such as [[Protein Explorer]] unable to deal properly with the remediated nucleic acids. | Here are some examples of changes that occurred in remediations affecting the PDB format. | ||
* '''DNA:''' Prior to August, 2007, both DNA and RNA nucleotides were named A, C, G, T, and U. After August, 2007, DNA nucleotides were changed to DA, DC, DG, DT and DU, while RNA nucleotides continued to use the older one-letter names. (An example of a model that contains both DNA and RNA is [[104d]].) This change required changes in software packages such as [[Jmol]], and left unmaintained packages such as [[Protein Explorer]] unable to deal properly with the remediated nucleic acids. | |||
* '''Non-standard residues''': Some PDB files represented non-standard residues as a standard residue (ATOM records) plus an adduct (HETATM records). Some of these were changed to a uniform name for a non-standard residue, so that all atoms in the same residue have the same name (and all are HETATM records). For example, phosphoserine in [[1apm]] was SER plus PHO; phosphothreonine THR plus PHO. These were remediated to SEP and TPO. | |||
In the March, 2009 remediation, the order of chains and atoms changed in some PDB files in a non-systematic manner. This broke some scenes that had been saved in Proteopedia, and required redesign of some portions of Proteopedia (see [[Getting_Unremediated_PDB_Files#Proteopedia avoids remediation-related problems|Proteopedia avoids remediation-related problems]]). | In the March, 2009 remediation, the order of chains and atoms changed in some PDB files in a non-systematic manner. This broke some scenes that had been saved in Proteopedia, and required redesign of some portions of Proteopedia (see [[Getting_Unremediated_PDB_Files#Proteopedia avoids remediation-related problems|Proteopedia avoids remediation-related problems]]). | ||